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(-) Description

Title :  CRYSTAL STRUCTURE OF YVAD-CMK BOUND HUMAN LEGUMAIN (AEP) IN COMPLEX WITH COMPOUND 11
 
Authors :  E. Dall, K. Ye, H. Brandstetter
Date :  08 Sep 16  (Deposition) - 29 Mar 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Cysteine Protease, Allosteric Inhibitor, Asparaginyl Endopeptidase, Alzheimer'S Disease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Zhang, O. Obianyo, E. Dall, Y. Du, H. Fu, X. Liu, S. S. Kang, M. Song, S. P. Yu, C. Cabrele, M. Schubert, X. Li, J. Z. Wang, H. Brandstetter, K. Ye
Inhibition Of Delta-Secretase Improves Cognitive Functions In Mouse Models Of Alzheimer'S Disease.
Nat Commun V. 8 14740 2017
PubMed-ID: 28345579  |  Reference-DOI: 10.1038/NCOMMS14740

(-) Compounds

Molecule 1 - AC-TYR-VAL-ALA-ASP-CHLOROMETHYLKETONE
    ChainsC
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    Other DetailsAC-YVAD-CHLOROMETHYLEKETONE INHIBITOR
    SyntheticYES
 
Molecule 2 - LEGUMAIN
    ChainsA
    EC Number3.4.22.34
    EngineeredYES
    Expression SystemLEISHMANIA TARENTOLAE
    Expression System Taxid5689
    FragmentUNP RESIDUES 26-288
    GeneLGMN, PRSC1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymASPARAGINYL ENDOPEPTIDASE,PROTEASE,CYSTEINE 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric/Biological Unit (6, 8)
No.NameCountTypeFull Name
10QE1Mod. Amino AcidCHLOROMETHANE
23Y71Ligand/Ion7-(MORPHOLIN-4-YL)-2,1,3-BENZOXADIAZOL-4-AMINE
3ACE1Mod. Amino AcidACETYL GROUP
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SNN1Mod. Amino AcidL-3-AMINOSUCCINIMIDE
6SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:58 , ASN A:91 , LYS A:224 , ARG A:225 , HOH A:409 , HOH A:440binding site for residue SO4 A 303
2AC2SOFTWARETHR A:250 , HIS A:252 , LYS A:253binding site for residue SO4 A 304
3AC3SOFTWAREHIS A:252 , HIS A:256 , GLN A:269 , LYS A:273 , SER A:276binding site for residue 3Y7 A 305
4AC4SOFTWAREASN A:167 , HIS A:197 , PRO A:199 , ILE A:202 , HOH A:415 , HOH A:444binding site for Mono-Saccharide NAG A 301 bound to ASN A 167
5AC5SOFTWAREASP A:200 , ASN A:272 , THR A:274 , HOH A:414binding site for Mono-Saccharide NAG A 302 bound to ASN A 272

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LU9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LU9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LU9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LU9)

(-) Exons   (0, 0)

(no "Exon" information available for 5LU9)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhhhhhhhhhhhhhhhhhh..hhh.eeee..................................hhhhhhhhhhhhhhhhhhhhhh..............eeeeeee..ee..eee....eeehhhhhhhhhhhhhh....eeeeee...hhhhhh........eeeee.........eeeee....eeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lu9 A  26 GGKHWVVIVAGSNGWYNYRHQADACHAYQIIHRNGIPDEQIVVMMYDDIAYSEDNPTPGIVINRPNGTDVYQGVPKDYTGEDVTPQNFLAVLRGDAEAVKGIGSGKVLKSGPQDHVFIYFTdHGSTGILVFPNEDLHVKDLNETIHYMYKHKMYRKMVFYIEACESGSMMNHLPDNINVYATTAANPRESSYACYYDEKRSTYLGDWYSVNWMEDSDVEDLTKETLHKQYHLVKSHTQTSHVMQYGNKTISTMKVMQFQGMKR 288
                                    35        45        55        65        75        85        95       105       115       125       135       145 |     155       165       175       185       195       205       215       225       235       245       255       265       275       285   
                                                                                                                                                   147-SNN                                                                                                                                         

Chain C from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5lu9 C 300 xYVADx 305
                            |    |
                          300-ACE|
                               305-0QE

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5LU9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LU9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LU9)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LGMN_HUMAN | Q995384aw9 4awa 4awb 4fgu 4n6n 4n6o 5lu8 5lua 5lub

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LU9)